Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges

Abstract

Protein folding is a multi-micro second time scale event and involves many conformational transitions. Crucial conformational transitions responsible for biological functions of biomolecules are difficult to capture using current state-of-the-art molecular dynamics (MD) simulations. Protein folding, being a stochastic process, witnesses these transitions as rare events. Many new methodologies have been proposed for observing these rare events. In this work, a temperature-aided cascade MD is proposed as a technique for studying the conformational transitions. Folding studies for Engrailed homeodomain and Immunoglobulin domain B of protein A have been carried out. Using this methodology, the unfolded structures with RMSD of 20 Å were folded to a structure with RMSD of 2 Å. Three sets of cascade MD runs were carried out using implicit solvation, explicit solvation, and charge updation scheme. In the charge updation scheme, charges based on the conformation obtained are calculated and are updated in the topology file. In all the simulations, the structure of 2 Å was reached within a few nanoseconds using these methods. Umbrella sampling has been performed using snapshots from the temperature-aided cascade MD simulation trajectory to build an entire conformational transition pathway. The advantage of the method is that the possible pathways for a particular reaction can be explored within a short duration of simulation time and the disadvantage is that the knowledge of the start and end state is required. The charge updation scheme adds the polarization effects in the force fields. This improves the electrostatic interaction among the atoms, which may help the protein to fold faster.

The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium‐exchange NMR spectroscopy

“…This is thus the first report to demonstrate the presence of residual structures in BDPA in a concentrated denaturant at an amino‐acid residue resolution. The folding behavior of BDPA has been studied intensively in both real experiments (Gouda et al 1992 , 1998 ; Kato et al 1993 ; Deisenhofer 1981 ; Sato et al 2004 , 2006 ; Myers and Oas 2001 ; Arora et al 2004 ; Huang et al 2007 , 2009 ; Bottomley et al 1994 ; Bai et al 1997 ; Cedergren et al 1993 ; Dimitriadis et al 2004 ; Vu et al 2004 ; Davis et al 2015 ; Otosu et al 2017 ; Oikawa et al 2013 , 2015 ) and computational simulations (Garcia and Onuchic 2003 ; Lei et al 2008 ; Shao and Gao 2011 ; Shao and Zhu 2017 ; Jani et al 2016 ; Shao 2014 ; Skolnick et al 1993 ; Kolinski and Skolnick 1994 ; Boczko and Brooks 3rd. 1995 ; Guo et al 1997 ; Zhou and Karplus 1999 ; Alonso and Daggett 2000 ; Berriz and Shakhnovich 2001 ; Favrin et al 2002 ; Ghosh et al 2002 ; Islam et al 2002 ; Zhou and Linhananta 2002 ; Kussell et al 2002 ; Jang et al 2003 ).…”

“…The earlier studies of the BDPA folding were carried out on the basis of a simple two‐state model between the native (N) and the U states without any stable folding intermediate (Sato et al 2004 , 2006 ; Myers and Oas 2001 ; Arora et al 2004 ; Huang et al 2007 , 2009 ; Bottomley et al 1994 ; Bai et al 1997 ; Cedergren et al 1993 ; Dimitriadis et al 2004 ). However, recent experimental and computational studies have demonstrated the presence of an early α‐helical folding intermediate during the kinetic refolding of the protein, and have indicated distinct kinetic and thermodynamic stabilities among the three helices (Vu et al 2004 ; Davis et al 2015 ; Garcia and Onuchic 2003 ; Lei et al 2008 ; Shao and Gao 2011 ; Shao and Zhu 2017 ; Jani et al 2016 ; Shao 2014 ). In addition, analyses using fluorescence spectroscopic techniques have revealed the structural heterogeneity of unfolded BDPA in concentrated GdmCl, and have implied the presence of residual structures in the U state (Otosu et al 2017 ; Oikawa et al 2013 , 2015 ).…”

Protein–Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics

“…The outlier flooding method (OFLOOD) can also be considered an extension of PaCS-MD and uses outlier detection based on clustering. Temperature-aided cascade molecular dynamics enhances conformational sampling with independent MD simulations at different temperatures . Peng and Zhang developed the PaCS-Fit method to conduct selection based on experimental data and successfully applied it to fit small-angle X-ray scattering and electron microscopy data …”

“…Temperature-aided cascade molecular dynamics enhances conformational sampling with independent MD simulations at different temperatures. 27 Peng and Zhang developed the PaCS-Fit method to conduct selection based on experimental data and successfully applied it to fit small-angle X-ray scattering and electron microscopy data. 28 In this paper, we demonstrate that PaCS-MD can be used to simulate protein−ligand dissociation within tens of nanoseconds by employing a longer intermolecular distance as the target quantity for the selection of the initial structures without applying force bias.…”

Simultaneous Determination of Two Subdomain Folding Rates Using the “Transfer-Quench” Method

“…Recently, a single molecule study indicated that the folding pathway is heterogeneous and this heterogeneity is hidden in the apparent two-state behavior (17). Computational studies also disagree on the folding pathway of this model protein (29)(30)(31). In this report, we describe our methodology, show its applicability, and show that the first results are in line with the nucleationcondensation model (32).…”